react-cheminfo 0.23.0 → 0.25.0

package/lib/language/ui/SiteLanguage.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SiteLanguage.js","sourceRoot":"","sources":["../../../src/language/ui/SiteLanguage.tsx"],"names":[],"mappings":";AAEA,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAa/D;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAAC,KAAwB;IACnD,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAC;IAClC,OAAO,KAAC,mBAAmB,IAAC,KAAK,EAAE,KAAK,YAAG,QAAQ,GAAuB,CAAC;AAC7E,CAAC"}

package/lib/language/ui/index.d.ts

@@ -0,0 +1,4 @@
+export type { SiteLanguageProps } from './SiteLanguage.tsx';
+export { SiteLanguage } from './SiteLanguage.tsx';
+export { useSiteLanguage } from './siteLanguageContext.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/language/ui/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/language/ui/index.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAC5D,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,0BAA0B,CAAC"}

package/lib/language/ui/index.js

@@ -0,0 +1,3 @@
+export { SiteLanguage } from "./SiteLanguage.js";
+export { useSiteLanguage } from "./siteLanguageContext.js";
+//# sourceMappingURL=index.js.map

package/lib/language/ui/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/language/ui/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAoB,CAAC;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,0BAA0B,CAAC"}

package/lib/language/ui/siteLanguageContext.d.ts

@@ -0,0 +1,12 @@
+/** What a site declares the page is being read in. */
+export declare const SiteLanguageContext: import("react").Context<string | undefined>;
+/**
+ * The language a link out of this page should name.
+ *
+ * Under a `SiteLanguage` it is what the site declared. Without one it is
+ * whatever the address itself names, so a site that has not been told anything
+ * still passes on the language it was opened in.
+ * @returns The tag, or `undefined` when no language is to be carried.
+ */
+export declare function useSiteLanguage(): string | undefined;
+//# sourceMappingURL=siteLanguageContext.d.ts.map

package/lib/language/ui/siteLanguageContext.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"siteLanguageContext.d.ts","sourceRoot":"","sources":["../../../src/language/ui/siteLanguageContext.ts"],"names":[],"mappings":"AAIA,sDAAsD;AACtD,eAAO,MAAM,mBAAmB,6CAA+C,CAAC;AAEhF;;;;;;;GAOG;AACH,wBAAgB,eAAe,IAAI,MAAM,GAAG,SAAS,CAIpD"}

package/lib/language/ui/siteLanguageContext.js

@@ -0,0 +1,19 @@
+import { createContext, use } from 'react';
+import { readLanguageParam } from "../core/languageParam.js";
+/** What a site declares the page is being read in. */
+export const SiteLanguageContext = createContext(undefined);
+/**
+ * The language a link out of this page should name.
+ *
+ * Under a `SiteLanguage` it is what the site declared. Without one it is
+ * whatever the address itself names, so a site that has not been told anything
+ * still passes on the language it was opened in.
+ * @returns The tag, or `undefined` when no language is to be carried.
+ */
+export function useSiteLanguage() {
+    const declared = use(SiteLanguageContext);
+    if (declared !== undefined)
+        return declared;
+    return readLanguageParam(globalThis.location?.search ?? '');
+}
+//# sourceMappingURL=siteLanguageContext.js.map

package/lib/language/ui/siteLanguageContext.js.map

@@ -0,0 +1 @@
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package/lib/orbital/core/atomicOrbitals.d.ts

@@ -33,8 +33,16 @@ export interface AtomicOrbital {
     effectiveCharge: number;
     /** Shielding `S` those rules produced. */
     shielding: number;
-    /** `−13.6 Z_eff²/n²`, electronvolts. */
+    /** `−13.606 Z_eff²/n²`, electronvolts: one rydberg times `Z_eff²/n²`. */
     energy: number;
+    /**
+     * Energy to pull this electron off the atom, electronvolts: the difference
+     * of Slater total energies between the ion and the atom. `null` when the
+     * subshell is empty, there being no electron to remove. This, not
+     * {@link AtomicOrbital.energy}, is the number to compare with a measured
+     * ionisation energy — see `slaterEnergy.ts`.
+     */
+    removalEnergy: number | null;
     /** `n − ℓ − 1` spheres on which the wavefunction changes sign. */
     radialNodes: number;
     /** ℓ planes or cones on which it changes sign. */

package/lib/orbital/core/atomicOrbitals.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"atomicOrbitals.d.ts","sourceRoot":"","sources":["../../../src/orbital/core/atomicOrbitals.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAOH,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAC;AAS5D,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAKvD,2EAA2E;AAC3E,MAAM,WAAW,aAAa;IAC5B,8DAA8D;IAC9D,EAAE,EAAE,MAAM,CAAC;IACX,wCAAwC;IACxC,CAAC,EAAE,MAAM,CAAC;IACV,mEAAmE;IACnE,CAAC,EAAE,MAAM,CAAC;IACV,4DAA4D;IAC5D,QAAQ,EAAE,YAAY,CAAC;IACvB,sDAAsD;IACtD,KAAK,EAAE,MAAM,CAAC;IACd,mEAAmE;IACnE,SAAS,EAAE,MAAM,CAAC;IAClB,uCAAuC;IACvC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,oDAAoD;IACpD,eAAe,EAAE,MAAM,CAAC;IACxB,0CAA0C;IAC1C,SAAS,EAAE,MAAM,CAAC;IAClB,yEAAyE;IACzE,MAAM,EAAE,MAAM,CAAC;IACf;;;;;;OAMG;IACH,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,kEAAkE;IAClE,WAAW,EAAE,MAAM,CAAC;IACpB,kDAAkD;IAClD,YAAY,EAAE,MAAM,CAAC;IACrB,uBAAuB;IACvB,UAAU,EAAE,MAAM,CAAC;IACnB,2DAA2D;IAC3D,SAAS,EAAE,OAAO,CAAC;IACnB,sDAAsD;IACtD,SAAS,EAAE,OAAO,CAAC;CACpB;AAED,4CAA4C;AAC5C,MAAM,WAAW,oBAAoB;IACnC;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,YAAY,EAAE,MAAM,EACpB,OAAO,GAAE,oBAAyB,GACjC,aAAa,EAAE,CAgEjB;AAED;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,SAAS,aAAa,EAAE,EAClC,EAAE,EAAE,MAAM,GACT,aAAa,GAAG,IAAI,CAKtB;AAED;;;;GAIG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,aAAa,GACrB,oBAAoB,CAEtB;AAaD;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,SAAS,aAAa,EAAE,GACjC,MAAM,GAAG,IAAI,CAaf"}

package/lib/orbital/core/atomicOrbitals.js

@@ -16,6 +16,7 @@ import { meanRadius, orbitalEnergy, radialNodeCount } from "./hydrogenic.js";
 import { MINIMUM_CHARGE, defaultMaximumShell, hundDistribution, outermostShell, withoutOutermostElectron, } from "./occupancy.js";
 import { harmonicsOf, subshellLetter } from "./realHarmonics.js";
 import { slaterScreening } from "./screening.js";
+import { slaterRemovalEnergy } from "./slaterEnergy.js";
 /**
  * Every orbital of an element, in Madelung (roughly energetic) order.
  * @param atomicNumber - Proton count, 1 to 118.
@@ -52,6 +53,11 @@ export function atomicOrbitalsOf(atomicNumber, options = {}) {
             l: subshell.l,
             charge,
         };
+        // Once per subshell, not once per harmonic: the seven orbitals of an f
+        // subshell share one removal energy.
+        const removalEnergy = subshellElectrons === 0
+            ? null
+            : slaterRemovalEnergy(atomicNumber, configuration, subshell);
         const harmonics = harmonicsOf(subshell.l);
         const spread = hundDistribution(subshellElectrons, harmonics.length);
         for (let index = 0; index < harmonics.length; index++) {
@@ -67,6 +73,7 @@ export function atomicOrbitalsOf(atomicNumber, options = {}) {
                 effectiveCharge: charge,
                 shielding: screening.shielding,
                 energy: orbitalEnergy(parameters),
+                removalEnergy,
                 radialNodes: radialNodeCount(parameters),
                 angularNodes: subshell.l,
                 meanRadius: meanRadius(parameters),

package/lib/orbital/core/atomicOrbitals.js.map

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package/lib/orbital/core/hydrogenic.d.ts

@@ -37,7 +37,8 @@ export declare function radialNodeCount(parameters: HydrogenicParameters): numbe
  */
 export declare function meanRadius(parameters: HydrogenicParameters): number;
 /**
- * Orbital energy in the hydrogen-like model, `E = −13.6 Z²/n²` eV.
+ * Orbital energy in the hydrogen-like model, `E = −13.606 Z²/n²` eV — one
+ * rydberg times `Z²/n²`.
  * @param parameters - Which orbital.
  * @returns The energy in electronvolts, always negative.
  */

package/lib/orbital/core/hydrogenic.d.ts.map

@@ -1 +1 @@
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package/lib/orbital/core/hydrogenic.js

@@ -36,7 +36,8 @@ export function meanRadius(parameters) {
         (2 * Math.max(charge, 1e-6)));
 }
 /**
- * Orbital energy in the hydrogen-like model, `E = −13.6 Z²/n²` eV.
+ * Orbital energy in the hydrogen-like model, `E = −13.606 Z²/n²` eV — one
+ * rydberg times `Z²/n²`.
  * @param parameters - Which orbital.
  * @returns The energy in electronvolts, always negative.
  */

package/lib/orbital/core/hydrogenic.js.map

@@ -1 +1 @@
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package/lib/orbital/core/index.d.ts

@@ -23,4 +23,5 @@ export type { AtomicSampleRequest, AtomicSampleResult, AtomicSampler, } from './
 export { runAtomicSample } from './sample.ts';
 export type { Screening } from './screening.ts';
 export { groupRank, slaterScreening } from './screening.ts';
+export { slaterRemovalEnergy, slaterTotalEnergy } from './slaterEnergy.ts';
 //# sourceMappingURL=index.d.ts.map

package/lib/orbital/core/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/orbital/core/index.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACxD,OAAO,EACL,oBAAoB,EACpB,4BAA4B,GAC7B,MAAM,iBAAiB,CAAC;AACzB,YAAY,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EACL,gBAAgB,EAChB,gBAAgB,EAChB,iBAAiB,EACjB,sBAAsB,GACvB,MAAM,qBAAqB,CAAC;AAC7B,YAAY,EAAE,IAAI,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,gBAAgB,CAAC;AACzE,YAAY,EAAE,QAAQ,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC9E,OAAO,EACL,iBAAiB,EACjB,qBAAqB,EACrB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,eAAe,EACf,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,EACf,WAAW,EACX,gBAAgB,EAChB,aAAa,GACd,MAAM,4BAA4B,CAAC;AACpC,YAAY,EAAE,OAAO,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,WAAW,CAAC;AACxE,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,WAAW,CAAC;AACpD,YAAY,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AACpD,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AAChF,YAAY,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAC;AAC5D,OAAO,EACL,oBAAoB,EACpB,eAAe,EACf,UAAU,EACV,aAAa,EACb,eAAe,EACf,eAAe,EACf,eAAe,EACf,aAAa,GACd,MAAM,iBAAiB,CAAC;AACzB,OAAO,EACL,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AACxB,YAAY,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AACxE,YAAY,EACV,kBAAkB,EAClB,yBAAyB,GAC1B,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAC7D,YAAY,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AACvD,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,WAAW,EACX,cAAc,GACf,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EACV,mBAAmB,EACnB,kBAAkB,EAClB,aAAa,GACd,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAC9C,YAAY,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAChD,OAAO,EAAE,SAAS,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAC5D,OAAO,EAAE,mBAAmB,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC"}

package/lib/orbital/core/index.js

@@ -11,4 +11,5 @@ export { radialDistribution } from "./radialDistribution.js";
 export { REAL_HARMONICS, SUBSHELL_LETTERS, harmonicsOf, subshellLetter, } from "./realHarmonics.js";
 export { runAtomicSample } from "./sample.js";
 export { groupRank, slaterScreening } from "./screening.js";
+export { slaterRemovalEnergy, slaterTotalEnergy } from "./slaterEnergy.js";
 //# sourceMappingURL=index.js.map

package/lib/orbital/core/index.js.map

@@ -1 +1 @@
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package/lib/orbital/core/slaterEnergy.d.ts

@@ -0,0 +1,35 @@
+/**
+ * What Slater's rules are actually good for: the energy it takes to pull one
+ * electron off the atom.
+ *
+ * The hydrogen-like orbital energy `−Ry Z_eff²/n²` is the model's own number
+ * and it orders the orbitals correctly, but it is not an ionisation energy and
+ * must never be read as one — it is 5.4× the measured value for neon, while
+ * being within 10% for lithium, so it is not even a constant factor off.
+ *
+ * Slater fitted his rules to *total* energies, and that is how they are used:
+ * add up `n Z_eff²/n²` over every electron of the atom, do the same for the ion
+ * with one electron gone — recomputing the shielding, which is the whole point,
+ * since the remaining electrons are screened by one fewer neighbour — and
+ * subtract. Over the first four periods that difference lands within a factor
+ * 0.74–1.81 of the measured first ionisation energy, against 0.9–5.4 for the
+ * orbital energy.
+ */
+import type { Subshell, SubshellOccupancy } from './electronConfiguration.ts';
+/**
+ * Total electronic energy of a configuration in the Slater model.
+ * @param atomicNumber - Proton count, the `Z` each electron is screened from.
+ * @param configuration - Every occupied subshell.
+ * @returns The sum of `−Ry Z_eff²/n²` over every electron, electronvolts.
+ */
+export declare function slaterTotalEnergy(atomicNumber: number, configuration: readonly SubshellOccupancy[]): number;
+/**
+ * Energy needed to take one electron out of a subshell and off the atom.
+ * @param atomicNumber - Proton count.
+ * @param configuration - Every occupied subshell of the neutral atom.
+ * @param subshell - The subshell the electron leaves.
+ * @returns `E(ion) − E(atom)`, electronvolts, positive for a bound electron.
+ * @throws {RangeError} When that subshell holds no electron to remove.
+ */
+export declare function slaterRemovalEnergy(atomicNumber: number, configuration: readonly SubshellOccupancy[], subshell: Subshell): number;
+//# sourceMappingURL=slaterEnergy.d.ts.map

package/lib/orbital/core/slaterEnergy.d.ts.map

@@ -0,0 +1 @@
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package/lib/orbital/core/slaterEnergy.js

@@ -0,0 +1,66 @@
+/**
+ * What Slater's rules are actually good for: the energy it takes to pull one
+ * electron off the atom.
+ *
+ * The hydrogen-like orbital energy `−Ry Z_eff²/n²` is the model's own number
+ * and it orders the orbitals correctly, but it is not an ionisation energy and
+ * must never be read as one — it is 5.4× the measured value for neon, while
+ * being within 10% for lithium, so it is not even a constant factor off.
+ *
+ * Slater fitted his rules to *total* energies, and that is how they are used:
+ * add up `n Z_eff²/n²` over every electron of the atom, do the same for the ion
+ * with one electron gone — recomputing the shielding, which is the whole point,
+ * since the remaining electrons are screened by one fewer neighbour — and
+ * subtract. Over the first four periods that difference lands within a factor
+ * 0.74–1.81 of the measured first ionisation energy, against 0.9–5.4 for the
+ * orbital energy.
+ */
+import { RYDBERG_ELECTRONVOLTS } from "./constants.js";
+import { slaterScreening } from "./screening.js";
+/**
+ * Total electronic energy of a configuration in the Slater model.
+ * @param atomicNumber - Proton count, the `Z` each electron is screened from.
+ * @param configuration - Every occupied subshell.
+ * @returns The sum of `−Ry Z_eff²/n²` over every electron, electronvolts.
+ */
+export function slaterTotalEnergy(atomicNumber, configuration) {
+    let energy = 0;
+    for (const occupied of configuration) {
+        const { effectiveCharge } = slaterScreening(atomicNumber, configuration, occupied);
+        energy -=
+            (occupied.electrons *
+                RYDBERG_ELECTRONVOLTS *
+                effectiveCharge *
+                effectiveCharge) /
+                (occupied.n * occupied.n);
+    }
+    return energy;
+}
+/**
+ * Energy needed to take one electron out of a subshell and off the atom.
+ * @param atomicNumber - Proton count.
+ * @param configuration - Every occupied subshell of the neutral atom.
+ * @param subshell - The subshell the electron leaves.
+ * @returns `E(ion) − E(atom)`, electronvolts, positive for a bound electron.
+ * @throws {RangeError} When that subshell holds no electron to remove.
+ */
+export function slaterRemovalEnergy(atomicNumber, configuration, subshell) {
+    const ion = [];
+    let found = false;
+    for (const occupied of configuration) {
+        if (occupied.n === subshell.n && occupied.l === subshell.l) {
+            found = true;
+            if (occupied.electrons === 1)
+                continue;
+            ion.push({ ...occupied, electrons: occupied.electrons - 1 });
+            continue;
+        }
+        ion.push(occupied);
+    }
+    if (!found) {
+        throw new RangeError(`the ${subshell.n}${'spdf'[subshell.l] ?? '?'} subshell holds no electron to remove`);
+    }
+    return (slaterTotalEnergy(atomicNumber, ion) -
+        slaterTotalEnergy(atomicNumber, configuration));
+}
+//# sourceMappingURL=slaterEnergy.js.map

package/lib/orbital/core/slaterEnergy.js.map

@@ -0,0 +1 @@
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package/lib/shared/ui/MenuButton.d.ts

@@ -3,8 +3,9 @@ import type { ReactElement } from 'react';
 /** What every button of a site header takes, whatever its menu holds. */
 export interface HeaderButtonProps {
     /**
-     * Whether the button is reduced to its icon — no text, no caret — for a
-     * header that has run out of room. The icon still opens the same menu.
+     * Whether the text is left out of the button altogether, rather than only
+     * hidden: a bar that has run out of room drops the caret with it. The glyph
+     * names itself through its tooltip either way.
      * @default false
      */
     compact?: boolean;

package/lib/shared/ui/MenuButton.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"MenuButton.d.ts","sourceRoot":"","sources":["../../../src/shared/ui/MenuButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAEpE,OAAO,KAAK,EAAiB,YAAY,EAAE,MAAM,OAAO,CAAC;AAQzD,yEAAyE;AACzE,MAAM,WAAW,iBAAiB;IAChC;;;;;OAKG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB;;;OAGG;IACH,SAAS,CAAC,EAAE,gBAAgB,CAAC,WAAW,CAAC,CAAC;CAC3C;AAED,sDAAsD;AACtD,MAAM,WAAW,eAAgB,SAAQ,iBAAiB;IACxD,6EAA6E;IAC7E,SAAS,EAAE,MAAM,CAAC;IAClB,2BAA2B;IAC3B,IAAI,EAAE,QAAQ,CAAC;IACf,6EAA6E;IAC7E,KAAK,EAAE,MAAM,CAAC;IACd,6BAA6B;IAC7B,IAAI,EAAE,YAAY,CAAC;CACpB;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,eAAe,GAAG,YAAY,CAwB/D"}

package/lib/shared/ui/MenuButton.js

@@ -13,6 +13,6 @@ const HOLDER_STYLE = {
  */
 export function MenuButton(props) {
     const { className, icon, label, menu, compact = false, placement = 'bottom-end', } = props;
-    return (_jsx("span", { className: className, style: HOLDER_STYLE, children: _jsx(PopoverNext, { placement: placement, content: menu, children: _jsx(Button, { variant: "minimal", icon: icon, endIcon: compact ? undefined : 'caret-down', text: compact ? undefined : label, "aria-label": label, title: compact ? label : undefined }) }) }));
+    return (_jsx("span", { className: className, style: HOLDER_STYLE, children: _jsx(PopoverNext, { placement: placement, content: menu, children: _jsx(Button, { variant: "minimal", icon: icon, endIcon: compact ? undefined : 'caret-down', text: compact ? undefined : label, "aria-label": label, title: label }) }) }));
 }
 //# sourceMappingURL=MenuButton.js.map

package/lib/shared/ui/MenuButton.js.map

@@ -1 +1 @@
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package/lib/structure/core/conformerMinimise.d.ts

@@ -0,0 +1,36 @@
+import type { Molecule } from 'openchemlib';
+import type { ConformerOptions } from './conformerOptions.ts';
+/**
+ * Relax one conformer in place and return its energy.
+ *
+ * Minimisation is best-effort. MMFF94 cannot type every element (boron, for
+ * one), so a conformer it refuses gets a `null` energy and a warning rather
+ * than an exception. A non-zero return code from `minimise()` is *not* a
+ * failure: ethyne returns 2 with a perfect geometry.
+ *
+ * Warnings count the conformers the generator handed back, kept or not, so one
+ * number never means two things — a row number would, once one is dropped.
+ * @param conformer - The conformer to relax. Mutated.
+ * @param options - Force field and iteration budget.
+ * @param produced - 1-based position of the conformer in the generator's output.
+ * @param warnings - Receives one sentence when the energy is unknown.
+ * @returns Total energy in kcal/mol, or `null` when none was computed.
+ */
+export declare function minimiseConformer(conformer: Molecule, options: ConformerOptions, produced: number, warnings: string[]): number | null;
+/** What {@link rankByEnergy} reads and rewrites on a conformer. */
+export interface RankedConformer {
+    id: number;
+    energy: number | null;
+    relativeEnergy: number | null;
+}
+/**
+ * Order a set from the most stable conformer down, number it from one in that
+ * order, and measure every known energy from the lowest.
+ *
+ * A conformer without an energy ranks after every one that has one; equal
+ * energies, and conformers without one, keep the order they came in.
+ * @param conformers - The set. Each `id` and `relativeEnergy` is rewritten in place.
+ * @returns The same conformers, most stable first.
+ */
+export declare function rankByEnergy<T extends RankedConformer>(conformers: readonly T[]): T[];
+//# sourceMappingURL=conformerMinimise.d.ts.map

package/lib/structure/core/conformerMinimise.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/conformerMinimise.js

@@ -0,0 +1,81 @@
+import { ForceFieldMMFF94 } from 'openchemlib';
+import { ordinal } from "../../format/core/words.js";
+/**
+ * Relax one conformer in place and return its energy.
+ *
+ * Minimisation is best-effort. MMFF94 cannot type every element (boron, for
+ * one), so a conformer it refuses gets a `null` energy and a warning rather
+ * than an exception. A non-zero return code from `minimise()` is *not* a
+ * failure: ethyne returns 2 with a perfect geometry.
+ *
+ * Warnings count the conformers the generator handed back, kept or not, so one
+ * number never means two things — a row number would, once one is dropped.
+ * @param conformer - The conformer to relax. Mutated.
+ * @param options - Force field and iteration budget.
+ * @param produced - 1-based position of the conformer in the generator's output.
+ * @param warnings - Receives one sentence when the energy is unknown.
+ * @returns Total energy in kcal/mol, or `null` when none was computed.
+ */
+export function minimiseConformer(conformer, options, produced, warnings) {
+    const algorithm = options.minimisation;
+    if (algorithm === 'none')
+        return null;
+    let energy;
+    try {
+        const forceField = new ForceFieldMMFF94(conformer, algorithm, {});
+        forceField.minimise({ maxIts: options.maxIterations });
+        energy = forceField.getTotalEnergy();
+    }
+    catch (error) {
+        warnings.push(`The ${ordinal(produced)} conformer produced could not be minimised with ${algorithm} (${readable(error)}), so its energy is unknown.`);
+        return null;
+    }
+    if (!Number.isFinite(energy)) {
+        warnings.push(`The ${ordinal(produced)} conformer produced minimised to a non-finite ${algorithm} energy, so its energy is unknown.`);
+        return null;
+    }
+    return energy;
+}
+/**
+ * Order a set from the most stable conformer down, number it from one in that
+ * order, and measure every known energy from the lowest.
+ *
+ * A conformer without an energy ranks after every one that has one; equal
+ * energies, and conformers without one, keep the order they came in.
+ * @param conformers - The set. Each `id` and `relativeEnergy` is rewritten in place.
+ * @returns The same conformers, most stable first.
+ */
+export function rankByEnergy(conformers) {
+    assignRelativeEnergies(conformers);
+    const ranked = conformers.toSorted(compareEnergy);
+    for (const [index, conformer] of ranked.entries())
+        conformer.id = index + 1;
+    return ranked;
+}
+function compareEnergy(a, b) {
+    if (a.energy === null)
+        return b.energy === null ? 0 : 1;
+    if (b.energy === null)
+        return -1;
+    return a.energy - b.energy;
+}
+function assignRelativeEnergies(conformers) {
+    let lowest = Number.POSITIVE_INFINITY;
+    for (const conformer of conformers) {
+        const energy = conformer.energy;
+        if (energy !== null && energy < lowest)
+            lowest = energy;
+    }
+    if (lowest === Number.POSITIVE_INFINITY)
+        return;
+    for (const conformer of conformers) {
+        const energy = conformer.energy;
+        if (energy !== null)
+            conformer.relativeEnergy = energy - lowest;
+    }
+}
+function readable(error) {
+    const message = error instanceof Error ? error.message : String(error);
+    return message.replace(/^\w+\$\w+: /, '');
+}
+//# sourceMappingURL=conformerMinimise.js.map

package/lib/structure/core/conformerMinimise.js.map

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package/lib/structure/core/conformerMinimum.d.ts

@@ -0,0 +1,62 @@
+import type { ConformerShape } from './conformerShape.ts';
+/** What {@link isKeptMinimum} and {@link minimisedShapes} read of a conformer. */
+export interface KeptConformer {
+    /** Total energy in kcal/mol, `null` when it was not computed. */
+    energy: number | null;
+    /** The 3D structure, as molfile text. */
+    molfile: {
+        data: string;
+    };
+}
+/**
+ * Energy gap, in kcal/mol, under which two minimised conformers can be the
+ * same minimum. Copies of one minimum agree to about 1e-7; distinct minima
+ * that close in energy differ in shape by more than a percent.
+ */
+export declare const SAME_ENERGY_TOLERANCE = 0.001;
+/** Gap between principal moments, relative to the largest, under which two shapes are one. */
+export declare const SAME_SHAPE_TOLERANCE = 0.001;
+/**
+ * Gap in chirality under which two shapes are one. Copies of one minimum agree
+ * to about 1e-4 and a shape that is its own mirror image reads within 1e-3 of
+ * zero, while the mirror images of a chiral minimum usually sit tenths apart.
+ */
+export declare const SAME_CHIRALITY_TOLERANCE = 0.01;
+/**
+ * Whether two minimised conformers are one energy minimum: the same energy,
+ * the same principal moments and the same chirality. The two mirror-image
+ * gauche butanes are two minima; the two chairs of cyclohexane, each its own
+ * mirror image, are one.
+ * @param energyA - Total energy of the first conformer, kcal/mol.
+ * @param shapeA - Shape of the first conformer.
+ * @param energyB - Total energy of the second conformer, kcal/mol.
+ * @param shapeB - Shape of the second conformer.
+ * @returns `true` when both agree within {@link SAME_ENERGY_TOLERANCE}, {@link SAME_SHAPE_TOLERANCE} and {@link SAME_CHIRALITY_TOLERANCE}.
+ */
+export declare function isSameMinimum(energyA: number, shapeA: ConformerShape, energyB: number, shapeB: ConformerShape): boolean;
+/**
+ * Whether two conformers have the same shape: the same principal moments and
+ * the same chirality, energies not consulted. Two mirror images share the
+ * moments and not the chirality, so they are two shapes.
+ * @param shapeA - Shape of one conformer.
+ * @param shapeB - Shape of the other.
+ * @returns `true` when both agree within {@link SAME_SHAPE_TOLERANCE} and {@link SAME_CHIRALITY_TOLERANCE}.
+ */
+export declare function isSameShape(shapeA: ConformerShape, shapeB: ConformerShape): boolean;
+/**
+ * Whether a minimised conformer lands in a minimum one of `kept` already holds.
+ * @param energy - Total energy of the candidate, kcal/mol.
+ * @param shape - Shape of the candidate.
+ * @param kept - The conformers kept so far.
+ * @param keptShapes - Their shapes, index for index; `null` where there is no energy.
+ * @returns `true` when one of them is the same minimum.
+ */
+export declare function isKeptMinimum(energy: number, shape: ConformerShape, kept: readonly KeptConformer[], keptShapes: ReadonlyArray<ConformerShape | null>): boolean;
+/**
+ * Shapes of conformers read back from their molfiles, so a continuation
+ * compares new conformers with the ones a previous run kept.
+ * @param conformers - Conformers of an earlier run.
+ * @returns Their shapes, index for index; `null` for one without an energy.
+ */
+export declare function minimisedShapes(conformers: readonly KeptConformer[]): Array<ConformerShape | null>;
+//# sourceMappingURL=conformerMinimum.d.ts.map

package/lib/structure/core/conformerMinimum.d.ts.map

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